1
|
Belyaeva J, Elgeti M. Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods. eLife 2024; 13:e99770. [PMID: 39283059 PMCID: PMC11405019 DOI: 10.7554/elife.99770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure-function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.
Collapse
Affiliation(s)
- Julia Belyaeva
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
- Institute for Medical Physics and Biophysics, Leipzig University Medical School, Leipzig, Germany
| | - Matthias Elgeti
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
- Institute for Medical Physics and Biophysics, Leipzig University Medical School, Leipzig, Germany
- Integrative Center for Bioinformatics, Leipzig University, Leipzig, Germany
| |
Collapse
|
2
|
Tessmer MH, Stoll S. chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling. PLoS Comput Biol 2023; 19:e1010834. [PMID: 37000838 PMCID: PMC10096462 DOI: 10.1371/journal.pcbi.1010834] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for electron paramagnetic resonance (EPR) spectroscopy, in particular double electron-electron resonance (DEER). It is based on in silico attachment of rotamer ensemble representations of spin labels to protein structures. chiLife enables the development of custom protein analysis and modeling pipelines using SDSL EPR experimental data. It allows the user to add custom spin labels, scoring functions and spin label modeling methods. chiLife is designed with integration into third-party software in mind, to take advantage of the diverse and rapidly expanding set of molecular modeling tools available with a Python interface. This article describes the main design principles of chiLife and presents a series of examples.
Collapse
Affiliation(s)
- Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| |
Collapse
|
3
|
Abstract
Growing evidence indicates that liquid-liquid phase separation (LLPS), a phenomenon whereby transient, weak interactions can facilitate self-assembly of proteins into liquid-like droplets and can contribute to the formation of amyloid fibrils. Such an observation has posited that LLPS and the associated formation of membrane-less organelles in the cell can contribute to protein aggregation in neurodegenerative disease. In this chapter, we describe methods for performing biophysical studies on the transactive response DNA-binding protein of 43 kDa (TDP-43), a protein that forms aggregates in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We describe purification of the disordered low-complexity domain (LCD) of TDP-43 and provide a methodology for studying the protein's behavior using site-directed spin labeling coupled with electron paramagnetic resonance. We additionally discuss visualization of TDP-43 LCD liquid droplets and methods for quantifying LLPS and aggregation into amyloid fibrils.
Collapse
Affiliation(s)
- W Michael Babinchak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
4
|
Babinchak WM, Haider R, Dumm BK, Sarkar P, Surewicz K, Choi JK, Surewicz WK. The role of liquid-liquid phase separation in aggregation of the TDP-43 low-complexity domain. J Biol Chem 2019; 294:6306-6317. [PMID: 30814253 PMCID: PMC6484124 DOI: 10.1074/jbc.ra118.007222] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Pathological aggregation of the transactive response DNA-binding protein of 43 kDa (TDP-43) is associated with several neurodegenerative disorders, including ALS, frontotemporal dementia, chronic traumatic encephalopathy, and Alzheimer's disease. TDP-43 aggregation appears to be largely driven by its low-complexity domain (LCD), which also has a high propensity to undergo liquid-liquid phase separation (LLPS). However, the mechanism of TDP-43 LCD pathological aggregation and, most importantly, the relationship between the aggregation process and LLPS remains largely unknown. Here, we show that amyloid formation by the LCD is controlled by electrostatic repulsion. We also demonstrate that the liquid droplet environment strongly accelerates LCD fibrillation and that its aggregation under LLPS conditions involves several distinct events, culminating in rapid assembly of fibrillar aggregates that emanate from within mature liquid droplets. These combined results strongly suggest that LLPS may play a major role in pathological TDP-43 aggregation, contributing to pathogenesis in neurodegenerative diseases.
Collapse
Affiliation(s)
- W Michael Babinchak
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Raza Haider
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Benjamin K Dumm
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Prottusha Sarkar
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krystyna Surewicz
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Jin-Kyu Choi
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| | - Witold K Surewicz
- From the Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
5
|
Zhang R, Sahu ID, Gibson KR, Muhammad NB, Bali AP, Comer RG, Liu L, Craig AF, Mccarrick RM, Dabney-Smith C, Sanders CR, Lorigan GA. Development of electron spin echo envelope modulation spectroscopy to probe the secondary structure of recombinant membrane proteins in a lipid bilayer. Protein Sci 2015; 24:1707-13. [PMID: 26355804 DOI: 10.1002/pro.2795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/24/2015] [Accepted: 08/25/2015] [Indexed: 12/19/2022]
Abstract
Membrane proteins conduct many important biological functions essential to the survival of organisms. However, due to their inherent hydrophobic nature, it is very difficult to obtain structural information on membrane-bound proteins using traditional biophysical techniques. We are developing a new approach to probe the secondary structure of membrane proteins using the pulsed EPR technique of Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopy. This method has been successfully applied to model peptides made synthetically. However, in order for this ESEEM technique to be widely applicable to larger membrane protein systems with no size limitations, protein samples with deuterated residues need to be prepared via protein expression methods. For the first time, this study shows that the ESEEM approach can be used to probe the local secondary structure of a (2) H-labeled d8 -Val overexpressed membrane protein in a membrane mimetic environment. The membrane-bound human KCNE1 protein was used with a known solution NMR structure to demonstrate the applicability of this methodology. Three different α-helical regions of KCNE1 were probed: the extracellular domain (Val21), transmembrane domain (Val50), and cytoplasmic domain (Val95). These results indicated α-helical structures in all three segments, consistent with the micelle structure of KCNE1. Furthermore, KCNE1 was incorporated into a lipid bilayer and the secondary structure of the transmembrane domain (Val50) was shown to be α-helical in a more native-like environment. This study extends the application of this ESEEM approach to much larger membrane protein systems that are difficult to study with X-ray crystallography and/or NMR spectroscopy.
Collapse
Affiliation(s)
- Rongfu Zhang
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Kaylee R Gibson
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Nefertiti B Muhammad
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Raven G Comer
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Lishan Liu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Andrew F Craig
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Robert M Mccarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Carole Dabney-Smith
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, 37232
| | - Gary A Lorigan
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, Ohio, 45056.,Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, 45056
| |
Collapse
|